122 lines
7.9 KiB
Python
122 lines
7.9 KiB
Python
# Common.smk ##########################################################################################################
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def infer_participant_platform(participant_file):
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with open(participant_file, encoding="ISO-8859-1") as external_file:
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external_file_content = external_file.readlines()
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platforms = external_file_content[1].strip().split(",")
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if platforms[0] == "multiple" or (len(platforms) > 1 and "android" in platforms and "ios" in platforms):
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platform = "android"
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else:
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platform = platforms[0]
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if platform not in ["android", "ios"]:
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raise ValueError("Platform (line 2) in a participant file should be 'android', 'ios', or 'multiple'. You typed '" + platforms + "'")
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return platform
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# Preprocessing.smk ####################################################################################################
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def optional_phone_sensed_bins_input(wildcards):
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platform = infer_participant_platform("data/external/"+wildcards.pid)
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if platform == "android":
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tables_platform = [table for table in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["IOS"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]]] # for android, discard any ios tables that may exist
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elif platform == "ios":
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tables_platform = [table for table in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["ANDROID"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"]]] # for ios, discard any android tables that may exist
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return expand("data/raw/{{pid}}/{table}_with_datetime.csv", table = tables_platform)
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# Features.smk #########################################################################################################
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def optional_ar_input(wildcards):
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platform = infer_participant_platform("data/external/"+wildcards.pid)
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if platform == "android":
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return ["data/raw/{pid}/" + config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"] + "_with_datetime_unified.csv",
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"data/processed/{pid}/" + config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"] + "_deltas.csv"]
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elif platform == "ios":
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return ["data/raw/{pid}/"+config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]+"_with_datetime_unified.csv",
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"data/processed/{pid}/"+config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]+"_deltas.csv"]
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def optional_conversation_input(wildcards):
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platform = infer_participant_platform("data/external/"+wildcards.pid)
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if platform == "android":
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return ["data/raw/{pid}/" + config["CONVERSATION"]["DB_TABLE"]["ANDROID"] + "_with_datetime_unified.csv"]
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elif platform == "ios":
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return ["data/raw/{pid}/" + config["CONVERSATION"]["DB_TABLE"]["IOS"] + "_with_datetime_unified.csv"]
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def optional_location_barnett_input(wildcards):
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if config["BARNETT_LOCATION"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED":
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return expand("data/raw/{{pid}}/{sensor}_resampled.csv", sensor=config["BARNETT_LOCATION"]["DB_TABLE"])
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else:
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return expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["BARNETT_LOCATION"]["DB_TABLE"])
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def optional_location_doryab_input(wildcards):
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if config["DORYAB_LOCATION"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED":
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return expand("data/raw/{{pid}}/{sensor}_resampled.csv", sensor=config["DORYAB_LOCATION"]["DB_TABLE"])
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else:
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return expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["DORYAB_LOCATION"]["DB_TABLE"])
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def optional_steps_sleep_input(wildcards):
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if config["STEP"]["EXCLUDE_SLEEP"]["EXCLUDE"] == True and config["STEP"]["EXCLUDE_SLEEP"]["TYPE"] == "FITBIT_BASED":
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return "data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv"
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else:
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return []
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def optional_wifi_input(wildcards):
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if len(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]) > 0 and len(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]) == 0:
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return {"visible_access_points": expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"])}
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elif len(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]) == 0 and len(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]) > 0:
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return {"connected_access_points": expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"])}
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elif len(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]) > 0 and len(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]) > 0:
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return {"visible_access_points": expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]), "connected_access_points": expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"])}
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else:
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raise ValueError("If you are computing WIFI features you need to provide either VISIBLE_ACCESS_POINTS, CONNECTED_ACCESS_POINTS or both")
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# Models.smk ###########################################################################################################
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def input_merge_features_of_single_participant(wildcards):
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if wildcards.source == "phone_fitbit_features":
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return expand("data/processed/{pid}/{features}_{day_segment}.csv", pid=wildcards.pid, features=config["PARAMS_FOR_ANALYSIS"]["PHONE_FEATURES"] + config["PARAMS_FOR_ANALYSIS"]["FITBIT_FEATURES"], day_segment=wildcards.day_segment)
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else:
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return expand("data/processed/{pid}/{features}_{day_segment}.csv", pid=wildcards.pid, features=config["PARAMS_FOR_ANALYSIS"][wildcards.source.upper()], day_segment=wildcards.day_segment)
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def optional_input_days_to_include(wildcards):
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if config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["ENABLED"]:
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# This input automatically trigers the rule days_to_analyse in mystudy.snakefile
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return ["data/interim/{pid}/days_to_analyse" + \
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"_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_BEFORE_SURGERY"]) + \
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"_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_IN_HOSPITAL"]) + \
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"_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_AFTER_DISCHARGE"]) + ".csv"]
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else:
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return []
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def optional_input_valid_sensed_days(wildcards):
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if config["PARAMS_FOR_ANALYSIS"]["DROP_VALID_SENSED_DAYS"]["ENABLED"]:
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# This input automatically trigers the rule phone_valid_sensed_days in preprocessing.snakefile
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return ["data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins.csv"]
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else:
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return []
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# Reports.smk ###########################################################################################################
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def optional_heatmap_days_by_sensors_input(wildcards):
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platform = infer_participant_platform("data/external/"+wildcards.pid)
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if platform == "android":
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tables_platform = [table for table in config["HEATMAP_DAYS_BY_SENSORS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["IOS"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]]] # for android, discard any ios tables that may exist
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elif platform == "ios":
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tables_platform = [table for table in config["HEATMAP_DAYS_BY_SENSORS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["ANDROID"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"]]] # for ios, discard any android tables that may exist
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return expand("data/raw/{{pid}}/{table}_with_datetime.csv", table = tables_platform)
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def find_day_segments_input_file(wildcards):
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for key, values in config.items():
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if "DB_TABLE" in config[key] and config[key]["DB_TABLE"] == wildcards.sensor:
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if "DAY_SEGMENTS" in config[key]:
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return config[key]["DAY_SEGMENTS"]
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else:
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raise ValueError("{} should have a DAY_SEGMENTS parameter containing the path to its day segments file".format(wildcards.sensor))
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